Last updated on 2026-02-10 17:51:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.2 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 1.2.2 | 5.49 | 78.30 | 83.79 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.2 | 15.00 | 172.28 | 187.28 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.2 | 14.00 | 176.21 | 190.21 | ERROR | |
| r-devel-windows-x86_64 | 1.2.2 | 12.00 | 123.00 | 135.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.2 | 8.26 | 109.16 | 117.42 | ERROR | |
| r-release-linux-x86_64 | 1.2.2 | 7.49 | 109.29 | 116.78 | ERROR | |
| r-release-macos-arm64 | 1.2.2 | NOTE | ||||
| r-release-macos-x86_64 | 1.2.2 | 6.00 | 114.00 | 120.00 | NOTE | |
| r-release-windows-x86_64 | 1.2.2 | 11.00 | 130.00 | 141.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.2.2 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.2.2 | 6.00 | 91.00 | 97.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.2.2 | 14.00 | 162.00 | 176.00 | ERROR |
Version: 1.2.2
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Ron Keizer <ronkeizer@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Ron",
family = "Keizer",
role = c("aut", "cre"),
email = "ronkeizer@gmail.com")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: Rd files
Result: NOTE
checkRd: (-1) new_vpc_theme.Rd:21: Lost braces; missing escapes or markup?
21 | \item{obs_color}: {color for observations points}
| ^
checkRd: (-1) new_vpc_theme.Rd:22: Lost braces; missing escapes or markup?
22 | \item{obs_size}: {size for observation points}
| ^
checkRd: (-1) new_vpc_theme.Rd:23: Lost braces; missing escapes or markup?
23 | \item{obs_median_color}: {color for median observation line}
| ^
checkRd: (-1) new_vpc_theme.Rd:24: Lost braces; missing escapes or markup?
24 | \item{obs_median_linetype}: {linetype for median observation line}
| ^
checkRd: (-1) new_vpc_theme.Rd:25: Lost braces; missing escapes or markup?
25 | \item{obs_median_size}: {size for median observation line}
| ^
checkRd: (-1) new_vpc_theme.Rd:26: Lost braces; missing escapes or markup?
26 | \item{obs_ci_fill}: {color for observation CI fill}
| ^
checkRd: (-1) new_vpc_theme.Rd:27: Lost braces; missing escapes or markup?
27 | \item{obs_ci_color}: {color for observation CI lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:28: Lost braces; missing escapes or markup?
28 | \item{obs_ci_linetype}: {linetype for observation CI lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:29: Lost braces; missing escapes or markup?
29 | \item{obs_ci_size}: {size for observations CI lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:30: Lost braces; missing escapes or markup?
30 | \item{sim_pi_fill}: {fill color for simulated prediction interval areas}
| ^
checkRd: (-1) new_vpc_theme.Rd:31: Lost braces; missing escapes or markup?
31 | \item{sim_pi_alpha}: {transparency for simulated prediction interval areas}
| ^
checkRd: (-1) new_vpc_theme.Rd:32: Lost braces; missing escapes or markup?
32 | \item{sim_pi_color}: {color for simulated prediction interval lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:33: Lost braces; missing escapes or markup?
33 | \item{sim_pi_linetype}: {linetype for simulated prediction interval lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:34: Lost braces; missing escapes or markup?
34 | \item{sim_pi_size}: {size for simulated prediction interval lines}
| ^
checkRd: (-1) new_vpc_theme.Rd:35: Lost braces; missing escapes or markup?
35 | \item{sim_median_fill}: {fill color for simulated median area}
| ^
checkRd: (-1) new_vpc_theme.Rd:36: Lost braces; missing escapes or markup?
36 | \item{sim_median_alpha}: {transparency for simulated median area}
| ^
checkRd: (-1) new_vpc_theme.Rd:37: Lost braces; missing escapes or markup?
37 | \item{sim_median_color}: {color for simulated median line}
| ^
checkRd: (-1) new_vpc_theme.Rd:38: Lost braces; missing escapes or markup?
38 | \item{sim_median_linetype}: {linetype for simulated median line}
| ^
checkRd: (-1) new_vpc_theme.Rd:39: Lost braces; missing escapes or markup?
39 | \item{sim_median_size}: {size for simulated median line}
| ^
checkRd: (-1) new_vpc_theme.Rd:40: Lost braces; missing escapes or markup?
40 | \item{bin_separators_color}: {color for bin separator lines, NA for don't plot}
| ^
checkRd: (-1) new_vpc_theme.Rd:41: Lost braces; missing escapes or markup?
41 | \item{bin_separators_location}: {where to plot bin separators ("t" for top, "b" for bottom)}
| ^
checkRd: (-1) new_vpc_theme.Rd:42: Lost braces; missing escapes or markup?
42 | \item{loq_color}: {color of line showing limit of quantification}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vpc_tte
> ### Title: VPC function for time-to-event (survival) data
> ### Aliases: vpc_tte
>
> ### ** Examples
>
> ## See vpc-docs.ronkeizer.com for more documentation and examples.
>
> ## Example for repeated) time-to-event data
> ## with NONMEM-like data (e.g. simulated using a dense grid)
>
> data(rtte_obs_nm)
> data(rtte_sim_nm)
>
> # treat RTTE as TTE, no stratification
> vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
new_vpc_theme 3.845 0.215 5.560
vpc_cens 3.775 0.032 5.011
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [12s/15s]
Running ‘test-filter_dv.R’ [1s/1s]
Running ‘test-labeller.R’ [6s/9s]
Running ‘test-scales.R’ [6s/9s]
Running ‘test-softwaretype.R’ [1s/2s]
Running ‘test-strat-col-detection.R’ [1s/2s]
Running ‘test-vpc.R’ [6s/7s]
Running ‘test-vpc_cat.R’ [3s/5s]
Running ‘test-vpc_cens.R’ [6s/9s]
Running ‘test-vpc_tte.R’ [2s/2s]
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vpc_tte
> ### Title: VPC function for time-to-event (survival) data
> ### Aliases: vpc_tte
>
> ### ** Examples
>
> ## See vpc-docs.ronkeizer.com for more documentation and examples.
>
> ## Example for repeated) time-to-event data
> ## with NONMEM-like data (e.g. simulated using a dense grid)
>
> data(rtte_obs_nm)
> data(rtte_sim_nm)
>
> # treat RTTE as TTE, no stratification
> vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [6s/7s]
Running ‘test-filter_dv.R’ [1s/1s]
Running ‘test-labeller.R’ [4s/5s]
Running ‘test-scales.R’ [4s/6s]
Running ‘test-softwaretype.R’ [1s/1s]
Running ‘test-strat-col-detection.R’ [1s/2s]
Running ‘test-vpc.R’ [4s/4s]
Running ‘test-vpc_cat.R’ [3s/3s]
Running ‘test-vpc_cens.R’ [4s/5s]
Running ‘test-vpc_tte.R’ [2s/2s]
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> ### Name: vpc_tte
> ### Title: VPC function for time-to-event (survival) data
> ### Aliases: vpc_tte
>
> ### ** Examples
>
> ## See vpc-docs.ronkeizer.com for more documentation and examples.
>
> ## Example for repeated) time-to-event data
> ## with NONMEM-like data (e.g. simulated using a dense grid)
>
> data(rtte_obs_nm)
> data(rtte_sim_nm)
>
> # treat RTTE as TTE, no stratification
> vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [17s/17s]
Running ‘test-filter_dv.R’
Running ‘test-labeller.R’
Running ‘test-scales.R’
Running ‘test-softwaretype.R’
Running ‘test-strat-col-detection.R’
Running ‘test-vpc.R’
Running ‘test-vpc_cat.R’
Running ‘test-vpc_cens.R’
Running ‘test-vpc_tte.R’
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [18s/22s]
Running ‘test-filter_dv.R’
Running ‘test-labeller.R’ [9s/10s]
Running ‘test-scales.R’ [9s/13s]
Running ‘test-softwaretype.R’
Running ‘test-strat-col-detection.R’
Running ‘test-vpc.R’ [9s/13s]
Running ‘test-vpc_cat.R’
Running ‘test-vpc_cens.R’ [9s/12s]
Running ‘test-vpc_tte.R’
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.2
Check: tests
Result: ERROR
Running 'test-add_sim_index_number.R' [9s]
Running 'test-filter_dv.R' [1s]
Running 'test-labeller.R' [5s]
Running 'test-scales.R' [5s]
Running 'test-softwaretype.R' [1s]
Running 'test-strat-col-detection.R' [1s]
Running 'test-vpc.R' [5s]
Running 'test-vpc_cat.R' [3s]
Running 'test-vpc_cens.R' [5s]
Running 'test-vpc_tte.R' [2s]
Running the tests in 'tests/test-add_sim_index_number.R' failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in 'tests/test-vpc_tte.R' failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vpc_tte
> ### Title: VPC function for time-to-event (survival) data
> ### Aliases: vpc_tte
>
> ### ** Examples
>
> ## See vpc-docs.ronkeizer.com for more documentation and examples.
>
> ## Example for repeated) time-to-event data
> ## with NONMEM-like data (e.g. simulated using a dense grid)
>
> data(rtte_obs_nm)
> data(rtte_sim_nm)
>
> # treat RTTE as TTE, no stratification
> vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
new_vpc_theme 3.348 0.147 5.201
Flavor: r-patched-linux-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [11s/15s]
Running ‘test-filter_dv.R’ [1s/2s]
Running ‘test-labeller.R’ [6s/7s]
Running ‘test-scales.R’ [6s/9s]
Running ‘test-softwaretype.R’ [1s/2s]
Running ‘test-strat-col-detection.R’ [1s/2s]
Running ‘test-vpc.R’ [5s/7s]
Running ‘test-vpc_cat.R’ [3s/3s]
Running ‘test-vpc_cens.R’ [6s/8s]
Running ‘test-vpc_tte.R’ [2s/3s]
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.2
Check: examples
Result: ERROR
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vpc_tte
> ### Title: VPC function for time-to-event (survival) data
> ### Aliases: vpc_tte
>
> ### ** Examples
>
> ## See vpc-docs.ronkeizer.com for more documentation and examples.
>
> ## Example for repeated) time-to-event data
> ## with NONMEM-like data (e.g. simulated using a dense grid)
>
> data(rtte_obs_nm)
> data(rtte_sim_nm)
>
> # treat RTTE as TTE, no stratification
> vpc_tte(sim = rtte_sim_nm[rtte_sim_nm$sim <= 20,],
+ obs = rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols=list(dv = "dv", idv = "t"), obs_cols=list(idv = "t"))
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
vpc 3.944 0.024 5.395
Flavor: r-release-linux-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running ‘test-add_sim_index_number.R’ [11s/15s]
Running ‘test-filter_dv.R’ [1s/1s]
Running ‘test-labeller.R’ [6s/8s]
Running ‘test-scales.R’ [6s/8s]
Running ‘test-softwaretype.R’ [1s/2s]
Running ‘test-strat-col-detection.R’ [1s/1s]
Running ‘test-vpc.R’ [5s/8s]
Running ‘test-vpc_cat.R’ [3s/4s]
Running ‘test-vpc_cens.R’ [6s/7s]
Running ‘test-vpc_tte.R’ [2s/3s]
Running the tests in ‘tests/test-add_sim_index_number.R’ failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in ‘tests/test-vpc_tte.R’ failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.2.2
Check: tests
Result: ERROR
Running 'test-add_sim_index_number.R' [13s]
Running 'test-filter_dv.R' [1s]
Running 'test-labeller.R' [7s]
Running 'test-scales.R' [7s]
Running 'test-softwaretype.R' [1s]
Running 'test-strat-col-detection.R' [1s]
Running 'test-vpc.R' [7s]
Running 'test-vpc_cat.R' [4s]
Running 'test-vpc_cens.R' [6s]
Running 'test-vpc_tte.R' [3s]
Running the tests in 'tests/test-add_sim_index_number.R' failed.
Complete output:
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Load the theophylline PK dataset
> obs <- Theoph
> colnames(obs) <- c("id", "wt", "dose", "time", "dv")
> obs <- obs %>%
+ dplyr::group_by(id) %>%
+ mutate(sex = round(runif(1))) # randomly assign a "sex" covariate
> sim <- sim_data(obs, # the design of the dataset
+ model = function(x) { # the model
+ vpc:::pk_oral_1cmt (t = x$time, dose=x$dose * x$wt, ka = x$ka, ke = x$ke, cl = x$cl * x$wt)
+ },
+ error = list(additive = 0.1),
+ theta = c(2.774, 0.0718, .0361), # parameter values
+ omega_mat = c(0.08854, # specified as lower triangle by default;
+ 0.02421, 0.02241, # note: assumed that every theta has iiv, set to 0 if no iiv.
+ 0.008069, 0.008639, 0.02862),
+ par_names = c("ka", "ke", "cl"), # link the parameters in the model to the thetas/omegas
+ n = 500)
Error:
! `arrange_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::sim_data(...)
2. │ └─tmp %>% dplyr::arrange_("sim", "id", "time")
3. └─dplyr::arrange_(., "sim", "id", "time")
4. └─dplyr:::lazy_defunct("arrange")
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Running the tests in 'tests/test-vpc_tte.R' failed.
Complete output:
> library(vpc)
> library(testit)
> Sys.setenv("R_TESTS" = "")
>
> ## Test for bug AR 20171025 column name simulation dataset
> test <- vpc::rtte_sim_nm[1:200000,]
> test$bla <- test$t
> test$t <- NULL
> obj <- vpc_tte(sim = test, # stratified for covariate and study arm
+ obs = vpc::rtte_obs_nm,
+ rtte = FALSE,
+ sim_cols = list(dv = "dv", idv = "bla"),
+ obs_cols = list(idv = "t"),
+ labeller = ggplot2::label_both)
Initializing.
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
Backtrace:
▆
1. ├─vpc::vpc_tte(...)
2. │ └─... %>% dplyr::filter(!duplicated(id))
3. ├─dplyr::filter(., !duplicated(id))
4. ├─dplyr::filter(., dv == 1 | last_obs == 1)
5. ├─dplyr::mutate(...)
6. └─dplyr::group_by_(., "id")
7. └─dplyr:::lazy_defunct("group_by")
8. └─lifecycle::deprecate_stop(...)
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
Execution halted
Flavor: r-oldrel-windows-x86_64
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